Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, Arkansas, United States of America.
PLoS One. 2013;8(3):e59224. doi: 10.1371/journal.pone.0059224. Epub 2013 Mar 14.
A database was constructed consisting of 45,923 Salmonella pulsed-field gel electrophoresis (PFGE) patterns. The patterns, randomly selected from all submissions to CDC PulseNet during 2005 to 2010, included the 20 most frequent serotypes and 12 less frequent serotypes. Meta-analysis was applied to all of the PFGE patterns in the database. In the range of 20 to 1100 kb, serotype Enteritidis averaged the fewest bands at 12 bands and Paratyphi A the most with 19, with most serotypes in the 13-15 range among the 32 serptypes. The 10 most frequent bands for each of the 32 serotypes were sorted and distinguished, and the results were in concordance with those from distance matrix and two-way hierarchical cluster analyses of the patterns in the database. The hierarchical cluster analysis divided the 32 serotypes into three major groups according to dissimilarity measures, and revealed for the first time the similarities among the PFGE patterns of serotype Saintpaul to serotypes Typhimurium, Typhimurium var. 5-, and I 4,[5],12:i:-; of serotype Hadar to serotype Infantis; and of serotype Muenchen to serotype Newport. The results of the meta-analysis indicated that the pattern similarities/dissimilarities determined the serotype discrimination of PFGE method, and that the possible PFGE markers may have utility for serotype identification. The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping.
构建了一个数据库，其中包含 45923 个沙门氏菌脉冲场凝胶电泳（PFGE）图谱。这些图谱是从 2005 年至 2010 年期间向 CDC PulseNet 提交的所有图谱中随机选择的，包括 20 种最常见的血清型和 12 种较少见的血清型。对数据库中的所有 PFGE 图谱进行了荟萃分析。在 20 至 1100kb 的范围内，肠炎沙门氏菌的平均条带数最少，为 12 条，而甲型副伤寒 A 的条带数最多，为 19 条，在 32 种血清型中，大多数血清型在 13-15 范围内。对 32 种血清型的每种最常见的 10 条带进行了排序和区分，结果与数据库中图谱的距离矩阵和双向层次聚类分析结果一致。层次聚类分析根据相似性度量将 32 种血清型分为三大组，首次揭示了血清型圣路易斯与血清型鼠伤寒、鼠伤寒 5-、I 4，[5]，12：i：-；血清型哈达尔与血清型肠炎；以及血清型慕尼黑与血清型纽波特之间的 PFGE 图谱的相似性。荟萃分析的结果表明，模式相似性/不相似性决定了 PFGE 方法的血清型鉴别能力，并且可能的 PFGE 标记物可能对血清型鉴定具有实用价值。独特的、血清型特异性的模式的存在可能为辅助人群中血清型的分布提供有用的信息，并可能减少对费力分析的需求，例如传统的血清分型。
